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Figure 5 | BMC Microbiology

Figure 5

From: Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates

Figure 5

Microheterogeneity in arginase sequences from clinical isolates of H. pylori. The arginase coding region (~1.0 kb) plus ~130 bp of the upstream region encompassing the promoter and 18 bp downstream were amplified by PCR using Pfx and cloned into pBluescript. The constructs were sequenced using T3 and T7-1 primers (see Materials and Methods). A. Summary of microheterogeneity in the arginase coding region in H. pylori. Multi-sequence pairwise alignments were conducted with the rocF coding region using ClustalW. The alignment was converted to a graphical representation to show regions that are 100% conserved (white) and regions that vary (black). B. Hypervariablity in the ~133 bp rocF upstream region including the arginase promoter sequence preceding the ATG start codon. Multi-sequence pairwise alignments of the ~133 bp rocF upstream region from H. pylori strains were conducted using ClustalW. The alignments were converted to a graphical representation to show regions that are 100% conserved (white) and regions that vary (black). The alignments revealed a hypervariable region proximal to the ATG start codon. Numbering based on that of H. pylori strain 26695. Underlined is the Shine-Dalgarno (SD) sequence. Numbers in parentheses correspond to the number of strains featuring the insertion (ins) or deletion (del). Strain AG1 was omitted from this analysis because its arginase upstream region was completely different from the other 22 strains. C. Hypervariability in the ~35 bp upstream of the arginase ATG translation start codon in 21 H. pylori strains. Some of the sequence hypervariability occurred in the predicted SD region (underlined). The consensus sequence for the 3' end of the 16S rRNA for H. pylori is shown, as well as the consensus SD sequence for other H. pylori genes. Arginase activity is shown on the right hand side in units rounded to the nearest 100. Asterisks indicate nucleotides conserved in all strains. D. Phylogram of RocF protein sequence from 23 H. pylori strains. ClustalX and Treeview were used to construct the tree. E. Phylogram of the rocF upstream region from 22 H. pylori strains. ClustalX and Treeview were used to construct the tree. Strain AG1 was omitted from this analysis because its arginase upstream region was completely different from the other 22 strains.

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